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- PDB-4ejz: Structure of MBOgg1 in complex with low affinity DNA ligand -

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Basic information

Entry
Database: PDB / ID: 4ejz
TitleStructure of MBOgg1 in complex with low affinity DNA ligand
Components
  • 3-Methyladenine DNA glycosylase
  • DNA (5'-D(*AP*GP*CP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*TP*AP*CP*C)-3')
  • DNA (5'-D(*T*GP*GP*TP*AP*GP*AP*CP*TP*TP*GP*GP*AP*CP*GP*C)-3')
KeywordsHYDROLASE/DNA / 8-oxoguanine DNA glycosylase / DNA / HYDROLASE-DNA complex
Function / homology
Function and homology information


oxidized purine nucleobase lesion DNA N-glycosylase activity / DNA-(apurinic or apyrimidinic site) lyase / nucleotide-excision repair / base-excision repair / damaged DNA binding
Similarity search - Function
TATA-Binding Protein - #260 / 8-oxoguanine DNA glycosylase, N-terminal / 8-oxoguanine DNA glycosylase, N-terminal domain / Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal) / Endonuclease Iii, domain 2 / Hypothetical protein; domain 2 / HhH-GPD superfamily base excision DNA repair protein / Helix-hairpin-helix, base-excision DNA repair, C-terminal / HhH-GPD domain / endonuclease III ...TATA-Binding Protein - #260 / 8-oxoguanine DNA glycosylase, N-terminal / 8-oxoguanine DNA glycosylase, N-terminal domain / Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal) / Endonuclease Iii, domain 2 / Hypothetical protein; domain 2 / HhH-GPD superfamily base excision DNA repair protein / Helix-hairpin-helix, base-excision DNA repair, C-terminal / HhH-GPD domain / endonuclease III / DNA glycosylase / Endonuclease III; domain 1 / TATA-Binding Protein / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA-(apurinic or apyrimidinic site) lyase
Similarity search - Component
Biological speciesThermoanaerobacter tengcongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsJiang, T. / Yu, H.J. / Bi, L.J. / Zhang, X.E. / Yang, M.Z.
CitationJournal: J.Struct.Biol. / Year: 2013
Title: Crystal structures of MBOgg1 in complex with two abasic DNA ligands
Authors: Yu, H.J. / Yang, M.Z. / Zhang, X.E. / Bi, L.J. / Jiang, T.
History
DepositionApr 8, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-Methyladenine DNA glycosylase
C: DNA (5'-D(*AP*GP*CP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*TP*AP*CP*C)-3')
D: DNA (5'-D(*T*GP*GP*TP*AP*GP*AP*CP*TP*TP*GP*GP*AP*CP*GP*C)-3')
B: 3-Methyladenine DNA glycosylase
E: DNA (5'-D(*AP*GP*CP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*TP*AP*CP*C)-3')
F: DNA (5'-D(*T*GP*GP*TP*AP*GP*AP*CP*TP*TP*GP*GP*AP*CP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)91,7076
Polymers91,7076
Non-polymers00
Water00
1
A: 3-Methyladenine DNA glycosylase
C: DNA (5'-D(*AP*GP*CP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*TP*AP*CP*C)-3')
D: DNA (5'-D(*T*GP*GP*TP*AP*GP*AP*CP*TP*TP*GP*GP*AP*CP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)45,8543
Polymers45,8543
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-14 kcal/mol
Surface area17320 Å2
MethodPISA
2
B: 3-Methyladenine DNA glycosylase
E: DNA (5'-D(*AP*GP*CP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*TP*AP*CP*C)-3')
F: DNA (5'-D(*T*GP*GP*TP*AP*GP*AP*CP*TP*TP*GP*GP*AP*CP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)45,8543
Polymers45,8543
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-13 kcal/mol
Surface area17340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.805, 103.596, 66.725
Angle α, β, γ (deg.)90.00, 90.65, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 3-Methyladenine DNA glycosylase / 8-oxoguanine-DNA-glycosylase


Mass: 36189.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter tengcongensis (bacteria)
Strain: MB4 / Gene: AlkA / Production host: Escherichia coli (E. coli)
References: UniProt: Q8R5T9, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: DNA chain DNA (5'-D(*AP*GP*CP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*TP*AP*CP*C)-3')


Mass: 4710.045 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*T*GP*GP*TP*AP*GP*AP*CP*TP*TP*GP*GP*AP*CP*GP*C)-3')


Mass: 4954.214 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.54 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 3500, 0.1-0.15M KH2PO4, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.0089 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jan 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0089 Å / Relative weight: 1
ReflectionResolution: 3.05→30 Å / Num. all: 14731 / Num. obs: 14731 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.125
Reflection shellResolution: 3.05→3.16 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.375 / Num. unique all: 1406 / % possible all: 93.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EJY

4ejy


Resolution: 3.05→30 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.85 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / ESU R Free: 0.596 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY. THE STRUCTURE WAS REFINED ALSO WITH PHENIX.REFINE.
RfactorNum. reflection% reflectionSelection details
Rfree0.29296 752 5.1 %RANDOM
Rwork0.25079 ---
all0.25282 13940 --
obs0.25282 13940 98.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 100.23 Å2 / Biso mean: 51.488 Å2 / Biso min: 26.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.89 Å20 Å22.92 Å2
2--3.45 Å20 Å2
3----5.28 Å2
Refinement stepCycle: LAST / Resolution: 3.05→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4718 1240 0 0 5958
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0226212
X-RAY DIFFRACTIONr_angle_refined_deg0.8692.2138651
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9865576
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.09724.142239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.7215856
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.6371528
X-RAY DIFFRACTIONr_chiral_restr0.0560.2944
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024290
X-RAY DIFFRACTIONr_mcbond_it0.2811.52860
X-RAY DIFFRACTIONr_mcangle_it0.50224637
X-RAY DIFFRACTIONr_scbond_it0.4433352
X-RAY DIFFRACTIONr_scangle_it0.8854.54014
LS refinement shellResolution: 3.045→3.123 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 58 -
Rwork0.359 933 -
all-991 -
obs--91 %

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